Prior to the founding of the diocese, the territory that made up the diocese at the time of its founding was under the jurisdiction of a number of different Catholic prelates. Most of these were purely academic as there was no Catholic presence in the area. Among the more notable of these was the Archdiocese of Saint Louis and the Dubuque Diocese. During this later period the church first came into the area with the arrival of missionaries and European settlers.

In February 1875 it was transferred from the ecclesiastical province of St. Louis to that of Milwaukee. Pope Leo XIII elevated the see to the rank of archdiocese on May 4, 1888 and its name was changed to reflect this. Pope Paul VI once again instituted a name change for the see on July 11, 1966. Reflecting the growth of the Catholic Church in the region, it became the Archdiocese of Saint Paul and Minneapolis, the name it retains today. His Excellency, the Most Reverend Archbishop John Clayton Nienstedt, succeeded to the post on the retirement of his predecessor, Archbishop Harry Flynn, on May 2, 2008.[2] However, in an effort to help the Archdiocese recover from criticisms he had faced for the handling of cases of sexual abuse of minors, in particular, the case of a now-laicized priest, and in the wake of unproven accusations against him that were found to not be substantial enough to proceed to trial, he resigned, along with one of his Auxiliary Bishops, Lee Piche, on Monday, June 15, 2015. Coadjutor Archbishop Bernard Hebda of Newark was named as the Apostolic Administrator of the Archdiocese by Pope Francis the same day, while retaining his other duties, until the appointment of Archbishop Emeritus Nienstedt's successor by the Pope.[3] On March 24, 2016, it was announced that Hebda was named as Archbishop of the Archdiocese and would cease as Coadjutor of Newark.[4]

In January 2015, the archdiocese filed for bankruptcy.[5] With the filing of bankruptcies by also the Diocese of Duluth and the Diocese of New Ulm, Minnesota set the record for having more Catholic bankruptcies than any other state in the United States of America.[6]